I didn't quite have any pets, but everyone in Skyloft had a Loftwing partner. [Smiling quietly, this guy is in the doorway with his Eevee on his shoulder. Carrying his egg still since it seems to need more time, there's a peeking top of egg sticking out from the blanket Link has it wrapped in.]

Though many of the Remlits there were pets to people in the academy and around the village.